From 8a6442acea7f3760ce62fdbfae0fe9635c378df7 Mon Sep 17 00:00:00 2001
From: Jonathan Weine <jweine@ethz.ch>
Date: Tue, 19 Mar 2024 12:05:07 +0100
Subject: [PATCH 01/27] Update breathing_motion_module notebook
---
notebooks/trajectory_modules/breathing_motion_module.ipynb | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/notebooks/trajectory_modules/breathing_motion_module.ipynb b/notebooks/trajectory_modules/breathing_motion_module.ipynb
index 6d19d23..7aa2b42 100644
--- a/notebooks/trajectory_modules/breathing_motion_module.ipynb
+++ b/notebooks/trajectory_modules/breathing_motion_module.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:a3586145ec8e482232ff0d175c210a9403945b1a3b86d6635ca7dcdd7b7c1e03
-size 12980893
+oid sha256:35bf6d74eada1aca889e0a3d5f062a6a0c26f14522a11077d89a7af7a3a99c58
+size 5934834
--
GitLab
From e30001162f55e8933c23133aa8c76d2dd8a3f10a Mon Sep 17 00:00:00 2001
From: Jonathan Weine <jweine@ethz.ch>
Date: Tue, 19 Mar 2024 13:13:35 +0100
Subject: [PATCH 02/27] Update cardiac_mesh_pod
---
notebooks/trajectory_modules/cardiac_mesh_pod.ipynb | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/notebooks/trajectory_modules/cardiac_mesh_pod.ipynb b/notebooks/trajectory_modules/cardiac_mesh_pod.ipynb
index 21f3b0b..3dcc1de 100644
--- a/notebooks/trajectory_modules/cardiac_mesh_pod.ipynb
+++ b/notebooks/trajectory_modules/cardiac_mesh_pod.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:84f0141bac2adcefaa3cc53f54a167c5e292f4ace19be013be28ec7824e2c576
-size 18265188
+oid sha256:1186f046fa5e43e027b7a318fc9e35571fd6418f17e449d3bbeb57e1caa3b025
+size 14123333
--
GitLab
From 93e505357aaa5e5ad0d3b54ebd830b9c6ccdc57d Mon Sep 17 00:00:00 2001
From: Jonathan Weine <jweine@ethz.ch>
Date: Tue, 19 Mar 2024 18:12:51 +0100
Subject: [PATCH 03/27] Update random motion trajectory notebook
Additionally fixed bug in CardiacMeshDataset introduced by changed pyvista definition
---
cmrsim/datasets/_cardiac_mesh.py | 4 ++--
notebooks/trajectory_modules/cardiac_mesh_pod.ipynb | 4 ++--
.../contracting_cardiac_mesh_with_random_disp.ipynb | 4 ++--
3 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/cmrsim/datasets/_cardiac_mesh.py b/cmrsim/datasets/_cardiac_mesh.py
index 8cae45e..5721fdf 100644
--- a/cmrsim/datasets/_cardiac_mesh.py
+++ b/cmrsim/datasets/_cardiac_mesh.py
@@ -56,7 +56,7 @@ class MeshDataset:
# pylint: disable=E1101
deformation_mesh = pyvista.UnstructuredGrid(
- {vtk.VTK_TETRA: self.mesh.cell_connectivity.reshape(-1, 4)},
+ {vtk.VTK_TETRA: self.mesh.cells.reshape(-1, 5)[:, 1:]},
reference_positions)
# Apply transformation for all time steps
@@ -200,7 +200,7 @@ class MeshDataset:
# pylint: disable=E1101
probing_mesh = pyvista.UnstructuredGrid(
- {vtk.VTK_TETRA: self.mesh.cell_connectivity.reshape(-1, 4)},
+ {vtk.VTK_TETRA: self.mesh.cells.reshape(-1, 5)[:, 1:]},
reference_positions)
probing_mesh = reference_mesh.probe(probing_mesh)
for name in field_names:
diff --git a/notebooks/trajectory_modules/cardiac_mesh_pod.ipynb b/notebooks/trajectory_modules/cardiac_mesh_pod.ipynb
index 3dcc1de..f31608e 100644
--- a/notebooks/trajectory_modules/cardiac_mesh_pod.ipynb
+++ b/notebooks/trajectory_modules/cardiac_mesh_pod.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:1186f046fa5e43e027b7a318fc9e35571fd6418f17e449d3bbeb57e1caa3b025
-size 14123333
+oid sha256:76ca9390f44b703043d57015c29d165e235b11327ddaffdab4ebfa6a538646ca
+size 14123286
diff --git a/notebooks/trajectory_modules/contracting_cardiac_mesh_with_random_disp.ipynb b/notebooks/trajectory_modules/contracting_cardiac_mesh_with_random_disp.ipynb
index 67f2601..5a6f830 100644
--- a/notebooks/trajectory_modules/contracting_cardiac_mesh_with_random_disp.ipynb
+++ b/notebooks/trajectory_modules/contracting_cardiac_mesh_with_random_disp.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:254275501dfc8af05decf03bc49f424767e1441f7642dd4f5d667a5132032202
-size 17627048
+oid sha256:573816a73c04364c5783a1302dc431a973b9ff3b5d5077cbcceebb9b1194344d
+size 17457606
--
GitLab
From 74fe4a0ab8a040cc0aab50d6167969f542a927a8 Mon Sep 17 00:00:00 2001
From: Jonathan Weine <jweine@ethz.ch>
Date: Tue, 19 Mar 2024 19:04:45 +0100
Subject: [PATCH 04/27] Updated taylor_trajectories notebook
---
notebooks/trajectory_modules/taylor_trajectories.ipynb | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/notebooks/trajectory_modules/taylor_trajectories.ipynb b/notebooks/trajectory_modules/taylor_trajectories.ipynb
index 5ae746c..cebfa4e 100644
--- a/notebooks/trajectory_modules/taylor_trajectories.ipynb
+++ b/notebooks/trajectory_modules/taylor_trajectories.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:6ce52c5e9cc0845d6bc4c2eff6100f9c96d14e571c16b22d4c5c8eff3c0843bf
-size 13255771
+oid sha256:85fc5747d6c50ecf22b65348a9096a7c29404e1dfb679cc094d13d2a8a75e927
+size 6542766
--
GitLab
From 56061ec7ca7ad734714cd5a83f5bee581e980235 Mon Sep 17 00:00:00 2001
From: Jonathan Weine <jweine@ethz.ch>
Date: Tue, 19 Mar 2024 19:44:21 +0100
Subject: [PATCH 05/27] Updated all trajectory module notebooks
---
notebooks/trajectory_modules/cardiac_mesh_pod.ipynb | 4 ++--
notebooks/trajectory_modules/flow_trajectory_module.ipynb | 4 ++--
notebooks/trajectory_modules/turbulent_flow.ipynb | 4 ++--
3 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/notebooks/trajectory_modules/cardiac_mesh_pod.ipynb b/notebooks/trajectory_modules/cardiac_mesh_pod.ipynb
index f31608e..9a8d846 100644
--- a/notebooks/trajectory_modules/cardiac_mesh_pod.ipynb
+++ b/notebooks/trajectory_modules/cardiac_mesh_pod.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:76ca9390f44b703043d57015c29d165e235b11327ddaffdab4ebfa6a538646ca
-size 14123286
+oid sha256:eb3d7ce0a295a68ddcfbd018c4e423298a75779d0ba0d30909273cdda4fca4ed
+size 14088078
diff --git a/notebooks/trajectory_modules/flow_trajectory_module.ipynb b/notebooks/trajectory_modules/flow_trajectory_module.ipynb
index 2312e92..8f0177e 100644
--- a/notebooks/trajectory_modules/flow_trajectory_module.ipynb
+++ b/notebooks/trajectory_modules/flow_trajectory_module.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:f4f8768cd61b257338cc1c779d1ab130a4243c53c18a89a2d957334a0a986ba4
-size 17426126
+oid sha256:514018be341822e8ca3bfd6c4b04bf7838944d67d8875f410d00668bc0ec456e
+size 17432232
diff --git a/notebooks/trajectory_modules/turbulent_flow.ipynb b/notebooks/trajectory_modules/turbulent_flow.ipynb
index 55bf1d2..975d3bb 100644
--- a/notebooks/trajectory_modules/turbulent_flow.ipynb
+++ b/notebooks/trajectory_modules/turbulent_flow.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:7b6b9ab88ef1f9b9269e74fc1802b8dea40a113c595041a939184eb2820b62d9
-size 1423425
+oid sha256:106071132844a022feef2b6d1f2f1f3bff0a03f4da1784ff978e57e46a6da256
+size 1545670
--
GitLab
From bf911685d6a14bea02810d128200068d92c0a663 Mon Sep 17 00:00:00 2001
From: Jonathan Weine <jweine@ethz.ch>
Date: Mon, 25 Mar 2024 13:07:11 +0100
Subject: [PATCH 06/27] Updated notebooks
---
notebooks/bloch_simulation/static_multi_coil_bssfp.ipynb | 4 ++--
notebooks/trajectory_modules/turbulent_flow.ipynb | 4 ++--
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/notebooks/bloch_simulation/static_multi_coil_bssfp.ipynb b/notebooks/bloch_simulation/static_multi_coil_bssfp.ipynb
index 8ea2978..0c32eaf 100644
--- a/notebooks/bloch_simulation/static_multi_coil_bssfp.ipynb
+++ b/notebooks/bloch_simulation/static_multi_coil_bssfp.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:d025dad54f823dfc15315d916ca2c6b3478c38bc45e3f4d5c008854ec947783c
-size 1803176
+oid sha256:c1bcfdc32f75b36340b5e6502918b95d9dbcd32deda2845e3b5f8f6c625311eb
+size 1327080
diff --git a/notebooks/trajectory_modules/turbulent_flow.ipynb b/notebooks/trajectory_modules/turbulent_flow.ipynb
index 975d3bb..1ae9f88 100644
--- a/notebooks/trajectory_modules/turbulent_flow.ipynb
+++ b/notebooks/trajectory_modules/turbulent_flow.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:106071132844a022feef2b6d1f2f1f3bff0a03f4da1784ff978e57e46a6da256
-size 1545670
+oid sha256:50dd9b7b00419da603048f9325070682b41307d466197ac8cd4513043493b638
+size 1400552
--
GitLab
From 12c14e52a0ebb8f2bb1f492e655db58a0351ebac Mon Sep 17 00:00:00 2001
From: Jonathan Weine <jweine@ethz.ch>
Date: Mon, 25 Mar 2024 13:56:31 +0100
Subject: [PATCH 07/27] Updated CPMG notebook
---
notebooks/bloch_simulation/static_CPMG_t2star.ipynb | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/notebooks/bloch_simulation/static_CPMG_t2star.ipynb b/notebooks/bloch_simulation/static_CPMG_t2star.ipynb
index dbb388b..c0ea5a8 100644
--- a/notebooks/bloch_simulation/static_CPMG_t2star.ipynb
+++ b/notebooks/bloch_simulation/static_CPMG_t2star.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:e6e6100c2e6e9cb049e92d544dc5cc881f2d1b988549476d39980ff5c7cde885
-size 73094
+oid sha256:deb5d97f256c92b233f94ec1b6e96b4f49fe6d3f55b0a64e77ea0b8323caafe1
+size 140848
--
GitLab
From f8c3e763d1e11a4fe90c8d31aa2c292c3cc29b59 Mon Sep 17 00:00:00 2001
From: Jonathan Weine <jweine@ethz.ch>
Date: Mon, 25 Mar 2024 13:57:24 +0100
Subject: [PATCH 08/27] Replaced deprecate pyvista.probe with .sample
See issue #181
---
cmrsim/datasets/_flow.py | 12 ++++++++----
cmrsim/datasets/_regular_grid.py | 21 +++++++++++++--------
notebooks/local_functions.py | 4 ++--
3 files changed, 23 insertions(+), 14 deletions(-)
diff --git a/cmrsim/datasets/_flow.py b/cmrsim/datasets/_flow.py
index 3cf2014..8be17cb 100644
--- a/cmrsim/datasets/_flow.py
+++ b/cmrsim/datasets/_flow.py
@@ -174,8 +174,10 @@ class RefillingFlowDataset(tf.Module):
gridded_seeding_volume = pyvista.ImageData(dimensions=dims + 1,
spacing=resolution,
origin=origin)
- self.gridded_seeding_volume = self.gridded_mesh.probe(gridded_seeding_volume)
-
+
+ # self.gridded_seeding_volume = self.gridded_mesh.probe(gridded_seeding_volume)
+ self.gridded_seeding_volume = gridded_seeding_volume.sample(self.gridded_mesh)
+
active_indx = np.where(self.gridded_seeding_volume.ptc().cell_data["in_mesh"] > 0.7)
active_cell_centers = self.gridded_seeding_volume.cell_centers().ptc().points[active_indx]
@@ -251,7 +253,8 @@ class RefillingFlowDataset(tf.Module):
# Re-seed particles in un-populated areas with Monte-Carlo rejection:
# 1. Estimate current particle density within slice
self._estimate_particle_density(residual_particle_pos[in_tolerance])
- sampled_particle_pos = self.gridded_seeding_volume.probe(sampled_particle_pos)
+ # sampled_particle_pos = self.gridded_seeding_volume.probe(sampled_particle_pos)
+ sampled_particle_pos = sampled_particle_pos.sample(self.gridded_seeding_volume)
density = np.array(sampled_particle_pos["density"])
decision_boundaries = density / particle_density
# 2. To prevent unintentionally increasing particle density, set the decision boundary
@@ -413,4 +416,5 @@ class RefillingFlowDataset(tf.Module):
smoothed_histogram = gaussian_filter(residual_histogram / sampling_volume,
sigma=sigma, truncate=2.5)
self.gridded_mesh.cell_data["density"] = smoothed_histogram.reshape(-1, order="F")
- return self.gridded_mesh.probe(self.original_mesh)
\ No newline at end of file
+ # return self.gridded_mesh.probe(self.original_mesh)
+ return self.original_mesh.sample(self.gridded_mesh)
\ No newline at end of file
diff --git a/cmrsim/datasets/_regular_grid.py b/cmrsim/datasets/_regular_grid.py
index f460738..99f035e 100644
--- a/cmrsim/datasets/_regular_grid.py
+++ b/cmrsim/datasets/_regular_grid.py
@@ -103,9 +103,10 @@ class RegularGridDataset:
readout_direction)
nbins = (field_of_view / spacing).m_as("dimensionless").astype(int)
new_slice = pyvista.ImageData(dimensions=nbins, spacing=spacing.m_as("m"),
- origin=-field_of_view.m_as("m") / 2)
+ origin=-field_of_view.m_as("m") / 2)
new_slice = new_slice.transform(total_transform, inplace=False)
- new_slice = self.mesh.probe(new_slice)
+ new_slice = new_slice.sample(self.mesh)
+ # new_slice = self.mesh.probe(new_slice)
if in_mps:
inv_transform = np.eye(4, 4)
@@ -123,7 +124,7 @@ class RegularGridDataset:
Assumes that the main magnetic field is pointing in z-direction of the contained mesh.
The susceptibility os assumed to be specified as parts per million
- (e.g. :math:`\chi_{air} = 0.36ppm`).
+ (e.g. :math:`\\chi_{air} = 0.36ppm`).
The result is store in self.mesh["offres"] and is also returned as Quantity.
@@ -163,8 +164,10 @@ class RegularGridDataset:
# ft_chi_3d_dual = tf.signal.fft3d(chi_3d + 1j * imaginary_channel)
ft_chi_3d_dual = tf.signal.fft3d(chi_3d)
# 2) multiplication with the dipole function
- dipole_kernel = self._compute_fourier_dipole_kernel(field_of_view,
- np.array(ft_chi_3d_dual.shape))
+ dipole_kernel = self._compute_fourier_dipole_kernel(
+ field_of_view,
+ np.array(ft_chi_3d_dual.shape))
+
ft_field_3d = ft_chi_3d_dual * dipole_kernel
# 3) inverse FT to spatial domain
field_3d_dual = tf.signal.ifft3d(ft_field_3d)
@@ -207,7 +210,8 @@ class RegularGridDataset:
r_min = np.min(input_mesh.points, axis=0) - padding.m_as("m") / 2
nbins = (Quantity(r_max - r_min, "m") / pixel_spacing.to("m")).m.astype(int)
mesh = pyvista.ImageData(dimensions=nbins, spacing=pixel_spacing.m_as("m"), origin=r_min)
- mesh = input_mesh.probe(mesh)
+ mesh = mesh.sample(input_mesh)
+ # mesh = input_mesh.probe(mesh)
return cls(mesh)
@classmethod
@@ -248,8 +252,9 @@ class RegularGridDataset:
shape = np.array(shapes[0][0:3])
origin = - pixel_spacing * shape / 2 + origin_offset
- mesh = pyvista.ImageData(dimensions=shape, spacing=pixel_spacing.m_as("m"),
- origin=origin.m_as("m"))
+ mesh = pyvista.ImageData(dimensions=shape,
+ spacing=pixel_spacing.m_as("m"),
+ origin=origin.m_as("m"))
for name, arr in data.items():
mesh[name] = arr.reshape([shape.prod(), *arr.shape[3:]], order="F")
diff --git a/notebooks/local_functions.py b/notebooks/local_functions.py
index d099780..c37a4f5 100644
--- a/notebooks/local_functions.py
+++ b/notebooks/local_functions.py
@@ -68,7 +68,7 @@ def create_cylinder_phantom(dimensions=(200, 200, 4), spacing=(0.001, 0.001, 0.0
:return: pyvista.UnstructuredGrid
"""
- raster = pyvista.UniformGrid(dimensions=dimensions, spacing=spacing, origin=-np.array(dimensions) * np.array(spacing) / 2)
+ raster = pyvista.ImageData(dimensions=dimensions, spacing=spacing, origin=-np.array(dimensions) * np.array(spacing) / 2)
cylinders = [pyvista.Cylinder(center=(*xy_positions[i].m_as("m"), 0.), direction=(0., 0., 1.), radius=radii[i].m_as("m"),)
for i in range(len(radii))]
max_radius = np.max(np.array(dimensions[0:2]) * np.array(spacing[0:2])) / 2
@@ -110,7 +110,7 @@ def create_spherical_phantom(dimensions=(120, 120, 120), spacing=(0.002, 0.002,
:param big_radius: float in meter
:return: pyvista.UnstructuredGrid
"""
- raster = pyvista.UniformGrid(dimensions=dimensions, spacing=spacing,
+ raster = pyvista.ImageData(dimensions=dimensions, spacing=spacing,
origin=-np.array(dimensions) * np.array(spacing) / 2)
sphere_big = pyvista.Sphere(radius=big_radius).extract_surface()
box = pyvista.Box(bounds=(-big_radius * 0.3, big_radius * 0.3, -big_radius/5,
--
GitLab
From 4ad249dcaf0c86364bb86dbaef19da4be95089f7 Mon Sep 17 00:00:00 2001
From: Jonathan Weine <jweine@ethz.ch>
Date: Mon, 25 Mar 2024 14:13:57 +0100
Subject: [PATCH 09/27] Reverted breaking change
---
cmrsim/datasets/_flow.py | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/cmrsim/datasets/_flow.py b/cmrsim/datasets/_flow.py
index 8be17cb..5f6bb11 100644
--- a/cmrsim/datasets/_flow.py
+++ b/cmrsim/datasets/_flow.py
@@ -172,8 +172,8 @@ class RefillingFlowDataset(tf.Module):
resolution = image_box / dims
origin = np.min(r_slice, axis=0)
gridded_seeding_volume = pyvista.ImageData(dimensions=dims + 1,
- spacing=resolution,
- origin=origin)
+ spacing=resolution,
+ origin=origin)
# self.gridded_seeding_volume = self.gridded_mesh.probe(gridded_seeding_volume)
self.gridded_seeding_volume = gridded_seeding_volume.sample(self.gridded_mesh)
@@ -253,8 +253,8 @@ class RefillingFlowDataset(tf.Module):
# Re-seed particles in un-populated areas with Monte-Carlo rejection:
# 1. Estimate current particle density within slice
self._estimate_particle_density(residual_particle_pos[in_tolerance])
- # sampled_particle_pos = self.gridded_seeding_volume.probe(sampled_particle_pos)
- sampled_particle_pos = sampled_particle_pos.sample(self.gridded_seeding_volume)
+ sampled_particle_pos = self.gridded_seeding_volume.probe(sampled_particle_pos)
+ # sampled_particle_pos = sampled_particle_pos.sample(self.gridded_seeding_volume)
density = np.array(sampled_particle_pos["density"])
decision_boundaries = density / particle_density
# 2. To prevent unintentionally increasing particle density, set the decision boundary
--
GitLab
From 3b891343cfd2e39853a99b1b8eccda31f4580a42 Mon Sep 17 00:00:00 2001
From: Jonathan Weine <jweine@ethz.ch>
Date: Mon, 25 Mar 2024 14:20:00 +0100
Subject: [PATCH 10/27] revert breaking changes
---
cmrsim/datasets/_flow.py | 14 +++++---------
1 file changed, 5 insertions(+), 9 deletions(-)
diff --git a/cmrsim/datasets/_flow.py b/cmrsim/datasets/_flow.py
index 5f6bb11..3cf2014 100644
--- a/cmrsim/datasets/_flow.py
+++ b/cmrsim/datasets/_flow.py
@@ -172,12 +172,10 @@ class RefillingFlowDataset(tf.Module):
resolution = image_box / dims
origin = np.min(r_slice, axis=0)
gridded_seeding_volume = pyvista.ImageData(dimensions=dims + 1,
- spacing=resolution,
- origin=origin)
-
- # self.gridded_seeding_volume = self.gridded_mesh.probe(gridded_seeding_volume)
- self.gridded_seeding_volume = gridded_seeding_volume.sample(self.gridded_mesh)
-
+ spacing=resolution,
+ origin=origin)
+ self.gridded_seeding_volume = self.gridded_mesh.probe(gridded_seeding_volume)
+
active_indx = np.where(self.gridded_seeding_volume.ptc().cell_data["in_mesh"] > 0.7)
active_cell_centers = self.gridded_seeding_volume.cell_centers().ptc().points[active_indx]
@@ -254,7 +252,6 @@ class RefillingFlowDataset(tf.Module):
# 1. Estimate current particle density within slice
self._estimate_particle_density(residual_particle_pos[in_tolerance])
sampled_particle_pos = self.gridded_seeding_volume.probe(sampled_particle_pos)
- # sampled_particle_pos = sampled_particle_pos.sample(self.gridded_seeding_volume)
density = np.array(sampled_particle_pos["density"])
decision_boundaries = density / particle_density
# 2. To prevent unintentionally increasing particle density, set the decision boundary
@@ -416,5 +413,4 @@ class RefillingFlowDataset(tf.Module):
smoothed_histogram = gaussian_filter(residual_histogram / sampling_volume,
sigma=sigma, truncate=2.5)
self.gridded_mesh.cell_data["density"] = smoothed_histogram.reshape(-1, order="F")
- # return self.gridded_mesh.probe(self.original_mesh)
- return self.original_mesh.sample(self.gridded_mesh)
\ No newline at end of file
+ return self.gridded_mesh.probe(self.original_mesh)
\ No newline at end of file
--
GitLab
From b4271b45a46f0d19d6f06389aebb65eec5189352 Mon Sep 17 00:00:00 2001
From: Jonathan Weine <jweine@ethz.ch>
Date: Thu, 11 Apr 2024 11:17:37 +0200
Subject: [PATCH 11/27] Updated static GRE shepp logan notebook
---
notebooks/bloch_simulation/static_CPMG_t2star.ipynb | 4 ++--
notebooks/bloch_simulation/static_cartesian_sGRE_shepp.ipynb | 4 ++--
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/notebooks/bloch_simulation/static_CPMG_t2star.ipynb b/notebooks/bloch_simulation/static_CPMG_t2star.ipynb
index c0ea5a8..4c56401 100644
--- a/notebooks/bloch_simulation/static_CPMG_t2star.ipynb
+++ b/notebooks/bloch_simulation/static_CPMG_t2star.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:deb5d97f256c92b233f94ec1b6e96b4f49fe6d3f55b0a64e77ea0b8323caafe1
-size 140848
+oid sha256:860ccac3d1f4243c86a7de2d8b05012d4653b579813c0c2b8a0719126d688816
+size 137377
diff --git a/notebooks/bloch_simulation/static_cartesian_sGRE_shepp.ipynb b/notebooks/bloch_simulation/static_cartesian_sGRE_shepp.ipynb
index 9e53352..f8229d3 100644
--- a/notebooks/bloch_simulation/static_cartesian_sGRE_shepp.ipynb
+++ b/notebooks/bloch_simulation/static_cartesian_sGRE_shepp.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:abb2f6223c8451ddefa4ef7a591d5555157f607e74428de730947246842ff18d
-size 928969
+oid sha256:e4bd34c845c0e2587e9e962a2217eae2b3c159c3d7e09ca3b726d8e7404814f5
+size 1555249
--
GitLab
From 66905aa02a419225540dfb001350c18c69e4110f Mon Sep 17 00:00:00 2001
From: Jonathan Weine <jweine@ethz.ch>
Date: Thu, 11 Apr 2024 11:54:34 +0200
Subject: [PATCH 12/27] Updated SS_EPI shepp logan notebook
---
notebooks/bloch_simulation/static_cartesian_SEEPI_shepp.ipynb | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/notebooks/bloch_simulation/static_cartesian_SEEPI_shepp.ipynb b/notebooks/bloch_simulation/static_cartesian_SEEPI_shepp.ipynb
index cd3e13f..0554459 100644
--- a/notebooks/bloch_simulation/static_cartesian_SEEPI_shepp.ipynb
+++ b/notebooks/bloch_simulation/static_cartesian_SEEPI_shepp.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:648096692b220ab320d00779c5e7ee13920aa655818767c450226e9e1b25c24d
-size 430074
+oid sha256:b1b111275d7ad422aa23b6fe7d16340051f60b977d8f3e48c52724d2e23d471d
+size 266713
--
GitLab
From 90cba0fa9b6efebfe43c8187fbf1cba83246149a Mon Sep 17 00:00:00 2001
From: Jonathan Weine <jweine@ethz.ch>
Date: Thu, 11 Apr 2024 11:55:01 +0200
Subject: [PATCH 13/27] removed typo
---
notebooks/bloch_simulation/static_cartesian_SEEPI_shepp.ipynb | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/notebooks/bloch_simulation/static_cartesian_SEEPI_shepp.ipynb b/notebooks/bloch_simulation/static_cartesian_SEEPI_shepp.ipynb
index 0554459..d703f11 100644
--- a/notebooks/bloch_simulation/static_cartesian_SEEPI_shepp.ipynb
+++ b/notebooks/bloch_simulation/static_cartesian_SEEPI_shepp.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:b1b111275d7ad422aa23b6fe7d16340051f60b977d8f3e48c52724d2e23d471d
-size 266713
+oid sha256:06b8f534f078e671955cedf52427dc1428e49a017f3975bccd56cf6ae8561f68
+size 266719
--
GitLab
From 4e8bbbc62c01eb924a519fc6ebbd14e8ab567a34 Mon Sep 17 00:00:00 2001
From: Jonathan Weine <jweine@ethz.ch>
Date: Thu, 11 Apr 2024 13:54:55 +0200
Subject: [PATCH 14/27] updated bssfp offress notebook
---
notebooks/bloch_simulation/static_BSSFP_offresonance.ipynb | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/notebooks/bloch_simulation/static_BSSFP_offresonance.ipynb b/notebooks/bloch_simulation/static_BSSFP_offresonance.ipynb
index ba22b48..9aef2dd 100644
--- a/notebooks/bloch_simulation/static_BSSFP_offresonance.ipynb
+++ b/notebooks/bloch_simulation/static_BSSFP_offresonance.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:b7c61f5259b8763f53cdb4bda406e6d6a298398f10b648218a8c02bc3da2c224
-size 919330
+oid sha256:934f14e79d779801c2857d48973003540c644ec080233d745208c731c0de1e61
+size 1160455
--
GitLab
From 5958f3643656940b6b22747d7475bc74eaebe95b Mon Sep 17 00:00:00 2001
From: Jonathan Weine <jweine@ethz.ch>
Date: Thu, 11 Apr 2024 18:33:46 +0200
Subject: [PATCH 15/27] Updated simple example from paper
---
notebooks/bloch_simulation/movmesh_bssfp.ipynb | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/notebooks/bloch_simulation/movmesh_bssfp.ipynb b/notebooks/bloch_simulation/movmesh_bssfp.ipynb
index c68ff5b..bc53407 100644
--- a/notebooks/bloch_simulation/movmesh_bssfp.ipynb
+++ b/notebooks/bloch_simulation/movmesh_bssfp.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:97cfc4518fe865454384402b4e822c4516795453c2b54a1f5e8ab1923970d9c1
-size 2666390
+oid sha256:171b06ac848ff03994b8fe9374ded3dd7f958933decad7c35757ae3983123e05
+size 2733609
--
GitLab
From 1b5ef5e1ff9541bc86cd27d4a39972df06d85743 Mon Sep 17 00:00:00 2001
From: Jonathan Weine <jweine@ethz.ch>
Date: Thu, 11 Apr 2024 22:09:05 +0200
Subject: [PATCH 16/27] Update turbulent flow notebook
---
notebooks/bloch_simulation/flow_venc_sGRE_turbUBend.ipynb | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/notebooks/bloch_simulation/flow_venc_sGRE_turbUBend.ipynb b/notebooks/bloch_simulation/flow_venc_sGRE_turbUBend.ipynb
index c038395..cb544a2 100644
--- a/notebooks/bloch_simulation/flow_venc_sGRE_turbUBend.ipynb
+++ b/notebooks/bloch_simulation/flow_venc_sGRE_turbUBend.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:b34dfa25b129eeba56c9ce378bb11a98aef853f41ded6ae759a305e28d4de01b
-size 7080260
+oid sha256:64fc9ecb3da8ca9cc24a2b8687a26302564b82f606bb84bd6a26e48123a1832a
+size 6371687
--
GitLab
From 327684a2bd0a2fa901f8b254d8fe2b8609252787 Mon Sep 17 00:00:00 2001
From: Jonathan Weine <jweine@ethz.ch>
Date: Fri, 12 Apr 2024 10:21:14 +0200
Subject: [PATCH 17/27] Replaced all occurances of .probe with .sample
Future deprecation of .probe is announced by pyvista, the recommended replacement is .sample
---
cmrsim/datasets/_flow.py | 9 ++++++---
1 file changed, 6 insertions(+), 3 deletions(-)
diff --git a/cmrsim/datasets/_flow.py b/cmrsim/datasets/_flow.py
index 3cf2014..5eed8ae 100644
--- a/cmrsim/datasets/_flow.py
+++ b/cmrsim/datasets/_flow.py
@@ -174,7 +174,8 @@ class RefillingFlowDataset(tf.Module):
gridded_seeding_volume = pyvista.ImageData(dimensions=dims + 1,
spacing=resolution,
origin=origin)
- self.gridded_seeding_volume = self.gridded_mesh.probe(gridded_seeding_volume)
+ # self.gridded_seeding_volume = self.gridded_mesh.probe(gridded_seeding_volume)
+ self.gridded_seeding_volume = gridded_seeding_volume.sample(self.gridded_mesh)
active_indx = np.where(self.gridded_seeding_volume.ptc().cell_data["in_mesh"] > 0.7)
active_cell_centers = self.gridded_seeding_volume.cell_centers().ptc().points[active_indx]
@@ -251,7 +252,8 @@ class RefillingFlowDataset(tf.Module):
# Re-seed particles in un-populated areas with Monte-Carlo rejection:
# 1. Estimate current particle density within slice
self._estimate_particle_density(residual_particle_pos[in_tolerance])
- sampled_particle_pos = self.gridded_seeding_volume.probe(sampled_particle_pos)
+ # sampled_particle_pos = self.gridded_seeding_volume.probe(sampled_particle_pos)
+ sampled_particle_pos = pyvista.PointSet(sampled_particle_pos).sample(self.gridded_seeding_volume)
density = np.array(sampled_particle_pos["density"])
decision_boundaries = density / particle_density
# 2. To prevent unintentionally increasing particle density, set the decision boundary
@@ -413,4 +415,5 @@ class RefillingFlowDataset(tf.Module):
smoothed_histogram = gaussian_filter(residual_histogram / sampling_volume,
sigma=sigma, truncate=2.5)
self.gridded_mesh.cell_data["density"] = smoothed_histogram.reshape(-1, order="F")
- return self.gridded_mesh.probe(self.original_mesh)
\ No newline at end of file
+ return self.original_mesh.sample(self.gridded_mesh)
+ # return self.gridded_mesh.probe(self.original_mesh)
\ No newline at end of file
--
GitLab
From 85bf59cd1a7413adc2927c76aa5799e96497164d Mon Sep 17 00:00:00 2001
From: Jonathan Weine <jweine@ethz.ch>
Date: Fri, 12 Apr 2024 10:22:06 +0200
Subject: [PATCH 18/27] Updated and improved laminar flow with sequental call
notebook
---
.../bloch_simulation/flow_venc_sGRE_stenosis_sequential.ipynb | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/notebooks/bloch_simulation/flow_venc_sGRE_stenosis_sequential.ipynb b/notebooks/bloch_simulation/flow_venc_sGRE_stenosis_sequential.ipynb
index 2da49a6..0ae7f4d 100644
--- a/notebooks/bloch_simulation/flow_venc_sGRE_stenosis_sequential.ipynb
+++ b/notebooks/bloch_simulation/flow_venc_sGRE_stenosis_sequential.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:bf503ff29ee0534f69a43ba7fe5214b31c9e8d8ea43151b98b52f98cad40698a
-size 15541521
+oid sha256:7ab05a78ae8be2ac1310584434b29e0bd46985637f15b4b72188e5a42d1a9923
+size 654582
--
GitLab
From bf68462da69d1c1e8a7b34bcbbad1b2473e98a3a Mon Sep 17 00:00:00 2001
From: Jonathan Weine <jweine@ethz.ch>
Date: Fri, 12 Apr 2024 12:15:53 +0200
Subject: [PATCH 19/27] Updated parallel venc laminar flow notebook
---
.../bloch_simulation/flow_mvenc_sGRE_ubend_parallel.ipynb | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/notebooks/bloch_simulation/flow_mvenc_sGRE_ubend_parallel.ipynb b/notebooks/bloch_simulation/flow_mvenc_sGRE_ubend_parallel.ipynb
index a0e472c..5e6d5ab 100644
--- a/notebooks/bloch_simulation/flow_mvenc_sGRE_ubend_parallel.ipynb
+++ b/notebooks/bloch_simulation/flow_mvenc_sGRE_ubend_parallel.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:9ab1685f95db98146fe387453b034078b168a7f3c639b0dcbb0f9032c01c9927
-size 3628975
+oid sha256:6be5d373f0fa1b9b29c1b8cb0c32b3042d8f3e8e0b20390c3a843c1f9d3b3a50
+size 2209619
--
GitLab
From 844df969b724050605039749d9f53b86f65b1b91 Mon Sep 17 00:00:00 2001
From: Jonathan Weine <jweine@ethz.ch>
Date: Fri, 12 Apr 2024 13:24:25 +0200
Subject: [PATCH 20/27] updated flow bssp which needs a rerun after fixing
.sample bug
---
notebooks/bloch_simulation/flow_bssfp_submodules_aorta.ipynb | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/notebooks/bloch_simulation/flow_bssfp_submodules_aorta.ipynb b/notebooks/bloch_simulation/flow_bssfp_submodules_aorta.ipynb
index dfc5048..3f1f39f 100644
--- a/notebooks/bloch_simulation/flow_bssfp_submodules_aorta.ipynb
+++ b/notebooks/bloch_simulation/flow_bssfp_submodules_aorta.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:608c9bae48c6d237eb6c107244ca57fecefd8b661b35bb08e6ad2876095a3a66
-size 718553
+oid sha256:6b6b0bc98bf0640096c3b68a3d555da28ebb12e9fbf4b73fd39a770c4bbaf692
+size 994153
--
GitLab
From ddcf595098107181e33d854d899a19abeba5e670 Mon Sep 17 00:00:00 2001
From: Jonathan Weine <jweine@ethz.ch>
Date: Fri, 12 Apr 2024 21:05:37 +0200
Subject: [PATCH 21/27] Found the reason why the density was not preserved in
reseeding when using .sample
---
cmrsim/datasets/_flow.py | 19 +++++++------------
1 file changed, 7 insertions(+), 12 deletions(-)
diff --git a/cmrsim/datasets/_flow.py b/cmrsim/datasets/_flow.py
index 5eed8ae..305da0d 100644
--- a/cmrsim/datasets/_flow.py
+++ b/cmrsim/datasets/_flow.py
@@ -109,20 +109,18 @@ class RefillingFlowDataset(tf.Module):
uniformly gridded mesh
:return: None
"""
+ self.original_mesh = mesh.copy()
image_box = np.max(mesh.points, axis=0) - np.min(mesh.points, axis=0)
dims = (image_box / lookup_map_spacing).astype(int)
resolution = image_box / dims
origin = np.min(mesh.points, axis=0)
- uniform_grid = pyvista.ImageData(dimensions=dims,
- spacing=resolution,
- origin=origin)
+ uniform_grid = pyvista.ImageData(dimensions=dims, spacing=resolution, origin=origin)
self.lookup_map_spacing = lookup_map_spacing
-
- uniform_grid = uniform_grid.sample(mesh)
+ uniform_grid = uniform_grid.sample(mesh, mark_blank=False)
uniform_grid["in_mesh"] = np.array(uniform_grid["vtkValidPointMask"], dtype=np.float64)
self.gridded_mesh = uniform_grid
- self.original_mesh = mesh
+
print("Updated Mesh")
# pylint: disable=multiple-statements
@@ -172,10 +170,9 @@ class RefillingFlowDataset(tf.Module):
resolution = image_box / dims
origin = np.min(r_slice, axis=0)
gridded_seeding_volume = pyvista.ImageData(dimensions=dims + 1,
- spacing=resolution,
- origin=origin)
- # self.gridded_seeding_volume = self.gridded_mesh.probe(gridded_seeding_volume)
- self.gridded_seeding_volume = gridded_seeding_volume.sample(self.gridded_mesh)
+ spacing=resolution,
+ origin=origin)
+ self.gridded_seeding_volume = gridded_seeding_volume.sample(self.gridded_mesh, mark_blank=False)
active_indx = np.where(self.gridded_seeding_volume.ptc().cell_data["in_mesh"] > 0.7)
active_cell_centers = self.gridded_seeding_volume.cell_centers().ptc().points[active_indx]
@@ -252,7 +249,6 @@ class RefillingFlowDataset(tf.Module):
# Re-seed particles in un-populated areas with Monte-Carlo rejection:
# 1. Estimate current particle density within slice
self._estimate_particle_density(residual_particle_pos[in_tolerance])
- # sampled_particle_pos = self.gridded_seeding_volume.probe(sampled_particle_pos)
sampled_particle_pos = pyvista.PointSet(sampled_particle_pos).sample(self.gridded_seeding_volume)
density = np.array(sampled_particle_pos["density"])
decision_boundaries = density / particle_density
@@ -416,4 +412,3 @@ class RefillingFlowDataset(tf.Module):
sigma=sigma, truncate=2.5)
self.gridded_mesh.cell_data["density"] = smoothed_histogram.reshape(-1, order="F")
return self.original_mesh.sample(self.gridded_mesh)
- # return self.gridded_mesh.probe(self.original_mesh)
\ No newline at end of file
--
GitLab
From f6b8b64015d632c1b8803ad4836ae6129aa8d394 Mon Sep 17 00:00:00 2001
From: Jonathan Weine <jweine@ethz.ch>
Date: Fri, 12 Apr 2024 21:30:20 +0200
Subject: [PATCH 22/27] rerun with correct re-seeding
---
notebooks/bloch_simulation/flow_bssfp_submodules_aorta.ipynb | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/notebooks/bloch_simulation/flow_bssfp_submodules_aorta.ipynb b/notebooks/bloch_simulation/flow_bssfp_submodules_aorta.ipynb
index 3f1f39f..048a09b 100644
--- a/notebooks/bloch_simulation/flow_bssfp_submodules_aorta.ipynb
+++ b/notebooks/bloch_simulation/flow_bssfp_submodules_aorta.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:6b6b0bc98bf0640096c3b68a3d555da28ebb12e9fbf4b73fd39a770c4bbaf692
-size 994153
+oid sha256:cfbaf63e9a642a2d3bf56aa84084211d14ce4764c42dce40241d211118a65199
+size 979310
--
GitLab
From a613339b3fac9cae4d20ff927582a89fca50e023 Mon Sep 17 00:00:00 2001
From: Jonathan Weine <jweine@ethz.ch>
Date: Fri, 12 Apr 2024 22:16:09 +0200
Subject: [PATCH 23/27] finished bloch notebooks
---
notebooks/bloch_simulation/movmesh_bssfp.ipynb | 4 ++--
notebooks/bloch_simulation/movmesh_general_bloch.ipynb | 4 ++--
notebooks/datasets/cardiac_mesh_dataset.ipynb | 4 ++--
notebooks/datasets/refilling_flow_dataset.ipynb | 4 ++--
4 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/notebooks/bloch_simulation/movmesh_bssfp.ipynb b/notebooks/bloch_simulation/movmesh_bssfp.ipynb
index bc53407..19be967 100644
--- a/notebooks/bloch_simulation/movmesh_bssfp.ipynb
+++ b/notebooks/bloch_simulation/movmesh_bssfp.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:171b06ac848ff03994b8fe9374ded3dd7f958933decad7c35757ae3983123e05
-size 2733609
+oid sha256:9b8df2c2f6a698a5ce28a06441aacf5c3f93c3e95f723bc57ee8a9381e2aa552
+size 2639915
diff --git a/notebooks/bloch_simulation/movmesh_general_bloch.ipynb b/notebooks/bloch_simulation/movmesh_general_bloch.ipynb
index 0612af1..7ce68dd 100644
--- a/notebooks/bloch_simulation/movmesh_general_bloch.ipynb
+++ b/notebooks/bloch_simulation/movmesh_general_bloch.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:26802a84586ba0ce715b160d22f7a8255b625fd8ecbb1d7058cf7e3b67cfb0a2
-size 90998
+oid sha256:eca080b6452d59631ea97068fbcd817c6d3bb6c78d569e6075faabf1fd406c78
+size 90999
diff --git a/notebooks/datasets/cardiac_mesh_dataset.ipynb b/notebooks/datasets/cardiac_mesh_dataset.ipynb
index b7b8138..210e4c9 100644
--- a/notebooks/datasets/cardiac_mesh_dataset.ipynb
+++ b/notebooks/datasets/cardiac_mesh_dataset.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:7253e082a73975d3e7ea6dcdcd9fa607d3504a4abc5dbb29671071f435a195c5
-size 3793044
+oid sha256:051d57400cd087d33ba33b247fe86381a141a45294c1557187d6b39ebf32161d
+size 3821399
diff --git a/notebooks/datasets/refilling_flow_dataset.ipynb b/notebooks/datasets/refilling_flow_dataset.ipynb
index f8dbfc8..471205c 100644
--- a/notebooks/datasets/refilling_flow_dataset.ipynb
+++ b/notebooks/datasets/refilling_flow_dataset.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:996458fb864d8b98c10ab68c3222c062c4d1cf62260d439625973bcf4c94c37d
-size 279000
+oid sha256:b7ec7146a560f6ab24dca736b162b2ba868e4b11e7cd9b0285416ccafe4b7467
+size 646135
--
GitLab
From 6d69d14da477b502ad8288da26d1ff26b3a32209 Mon Sep 17 00:00:00 2001
From: Jonathan Weine <jweine@ethz.ch>
Date: Fri, 12 Apr 2024 22:16:43 +0200
Subject: [PATCH 24/27] Reran basic functionality notebook
---
notebooks/analytic_simulation/1_basic_functionality.ipynb | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/notebooks/analytic_simulation/1_basic_functionality.ipynb b/notebooks/analytic_simulation/1_basic_functionality.ipynb
index d87822c..f44430a 100644
--- a/notebooks/analytic_simulation/1_basic_functionality.ipynb
+++ b/notebooks/analytic_simulation/1_basic_functionality.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:6bf9680412df66ad08a714289785460b5ffa245712d0f966aafdbfae05a5efb8
-size 1219948
+oid sha256:c011ef80d4c1f1b5a6f5db422fcab9bbda77c632ef0721344a01f1a69b122729
+size 1306899
--
GitLab
From 616e7ec4ca18f7acfec0d36ea37cc2fba74c6713 Mon Sep 17 00:00:00 2001
From: Jonathan Weine <jweine@ethz.ch>
Date: Sun, 14 Apr 2024 21:56:32 +0200
Subject: [PATCH 25/27] Updated Bssf analytic notebook
---
cmrsim/analytic/encoding/_from_sequence.py | 13 +++++++------
.../analytic_simulation/1_basic_functionality.ipynb | 4 ++--
notebooks/analytic_simulation/2_motion.ipynb | 4 ++--
.../analytic_simulation/3_multiple_coils.ipynb | 4 ++--
.../analytic_simulation/BSSFP_offresonance.ipynb | 4 ++--
5 files changed, 15 insertions(+), 14 deletions(-)
diff --git a/cmrsim/analytic/encoding/_from_sequence.py b/cmrsim/analytic/encoding/_from_sequence.py
index f367999..c66df44 100644
--- a/cmrsim/analytic/encoding/_from_sequence.py
+++ b/cmrsim/analytic/encoding/_from_sequence.py
@@ -81,12 +81,13 @@ class GenericEncoding(BaseSampling):
_, k_adc, t_adc = seq.calculate_kspace()
k_space.append(k_adc.T)
timings.append(t_adc)
-
- # pylint: disable=no-value-for-parameter, unexpected-keyword-arg
- k_space = tf.cast(tf.concat(k_space, axis=0), tf.float32)
- # pylint: disable=no-value-for-parameter, unexpected-keyword-arg
- timings = tf.cast(tf.concat(timings, axis=0), tf.float32)
- return cls(name, k_space, timings, absolute_noise_std, k_space_segments, device)
+ k_space = np.concatenate(k_space, axis=0, dtype=np.float32)
+ timings = np.concatenate(timings, axis=0, dtype=np.float32)
+ # # pylint: disable=no-value-for-parameter, unexpected-keyword-arg
+ # k_space = tf.cast(tf.concat(k_space, axis=0), tf.float32)
+ # # pylint: disable=no-value-for-parameter, unexpected-keyword-arg
+ # timings = tf.cast(tf.concat(timings, axis=0), tf.float32)
+ return cls(name, [k_space, ], [timings, ], absolute_noise_std, k_space_segments, device)
def from_pulseq(self):
raise NotImplementedError("Pulseq interface not yet implemented")
\ No newline at end of file
diff --git a/notebooks/analytic_simulation/1_basic_functionality.ipynb b/notebooks/analytic_simulation/1_basic_functionality.ipynb
index f44430a..b4d0dd1 100644
--- a/notebooks/analytic_simulation/1_basic_functionality.ipynb
+++ b/notebooks/analytic_simulation/1_basic_functionality.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:c011ef80d4c1f1b5a6f5db422fcab9bbda77c632ef0721344a01f1a69b122729
-size 1306899
+oid sha256:b8d56d63e89341adc9e7ef890e94fa029b7ecc8cee5e87ed3944fef570ee7391
+size 1306438
diff --git a/notebooks/analytic_simulation/2_motion.ipynb b/notebooks/analytic_simulation/2_motion.ipynb
index b4c1cfe..f86ad21 100644
--- a/notebooks/analytic_simulation/2_motion.ipynb
+++ b/notebooks/analytic_simulation/2_motion.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:9f7ffbb659227027875a88243eb395255f03f7c19eeb248d4fa4d38f77990b3a
-size 3231222
+oid sha256:c0382e4d5c6832fa6d13c0c45a27c90314291aeeff35082cb0bbd747dc84aedf
+size 3150514
diff --git a/notebooks/analytic_simulation/3_multiple_coils.ipynb b/notebooks/analytic_simulation/3_multiple_coils.ipynb
index bbd815c..0952332 100644
--- a/notebooks/analytic_simulation/3_multiple_coils.ipynb
+++ b/notebooks/analytic_simulation/3_multiple_coils.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:daacf2559adad01b78ecf763ec4eaa6962edb47bd454064db07352ef5dc51610
-size 2568841
+oid sha256:277fa0161aa58d7ed2598f215a2355ede6f3977e4ef2695a701d4c55a9045521
+size 4888167
diff --git a/notebooks/analytic_simulation/BSSFP_offresonance.ipynb b/notebooks/analytic_simulation/BSSFP_offresonance.ipynb
index cd7b41c..96c4f98 100644
--- a/notebooks/analytic_simulation/BSSFP_offresonance.ipynb
+++ b/notebooks/analytic_simulation/BSSFP_offresonance.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:bb017045678b9a3a2299fa7512712d6d045d67a3edd5158adc6ca6d7cbb57964
-size 539217
+oid sha256:593385a3434d5cfd7ea952c1040b071d3074655c41b22144f71bae35db2e31f1
+size 705165
--
GitLab
From 96268e44d961193d97ac5c7a4fdfeb39b7aa7922 Mon Sep 17 00:00:00 2001
From: Jonathan Weine <jweine@ethz.ch>
Date: Sun, 14 Apr 2024 22:05:53 +0200
Subject: [PATCH 26/27] Integrated slice selective analytic into docs
---
docs/source/conf.py | 2 +-
notebooks/analytic_simulation/slice_profile_weighting.ipynb | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 299aecd..f3728a7 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -177,7 +177,7 @@ nbsphinx_thumbnails = {
'example_gallery/analytic_simulation/3_multiple_coils': '_static/notebook_thumbnails/analytic_multiple_coils.png',
'example_gallery/analytic_simulation/BSSFP_offresonance': '_static/notebook_thumbnails/analytic_static_bssfp.png',
'example_gallery/analytic_simulation/cardiac_dti_with_background': '_static/notebook_thumbnails/analytic_cdti_stylized.png',
- 'example_gallery/analytic_simulation/simulate_mrxcat_cmrsim': '_static/notebook_thumbnails/analytic_bssfp.svg',
+ 'example_gallery/analytic_simulation/slice_profile_weighting': '_static/notebook_thumbnails/analytic_slice_select.png',
# Bloch
'example_gallery/bloch_simulation/static_cartesian_SEEPI_shepp': '_static/notebook_thumbnails/static_bloch_epi.svg',
'example_gallery/bloch_simulation/static_cartesian_sGRE_shepp': '_static/notebook_thumbnails/static_bloch_spoiled_gre.svg',
diff --git a/notebooks/analytic_simulation/slice_profile_weighting.ipynb b/notebooks/analytic_simulation/slice_profile_weighting.ipynb
index ee90635..fc176be 100644
--- a/notebooks/analytic_simulation/slice_profile_weighting.ipynb
+++ b/notebooks/analytic_simulation/slice_profile_weighting.ipynb
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:d98481fc96d5498b6863c01f06366c84edf704bb555a610002f485c3132e7426
-size 795512
+oid sha256:ead40d9cec098416e02ae58bdf19c52a0eee73e4c197f1eb9f4b1ff94eece6b8
+size 584225
--
GitLab
From 4c78b1b059fbb860f112fca2092805765537bf9c Mon Sep 17 00:00:00 2001
From: Jonathan Weine <jweine@ethz.ch>
Date: Sun, 14 Apr 2024 22:06:38 +0200
Subject: [PATCH 27/27] added reduce retracing
---
cmrsim/trajectory/_proper_ortho_decomp.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/cmrsim/trajectory/_proper_ortho_decomp.py b/cmrsim/trajectory/_proper_ortho_decomp.py
index ce771cd..e9be968 100644
--- a/cmrsim/trajectory/_proper_ortho_decomp.py
+++ b/cmrsim/trajectory/_proper_ortho_decomp.py
@@ -194,7 +194,7 @@ class PODTrajectoryModule(BaseTrajectoryModule):
return tf.ensure_shape(data[:, 0, :3], (None, 3)), additional_data
- @tf.function(jit_compile=False)
+ @tf.function(jit_compile=False, reduce_retracing=True)
def _evaluate_trajectory(self, t: tf.Tensor) -> tf.Tensor:
"""Reconstructs the data state at given times t, by evaluating the taylor series
of mode-weights and computing the weighted sum.
--
GitLab